The Vatican is facing a deepening controversy over the burial 22 years ago of a notorious crime boss, with reports emerging that the church accepted a one billion lire (£407,000) payment from the mobster's widow to allow his interment in a basilica.

A source at the Holy See told the Ansa news agency that "despite initial reluctance" the then vicar-general of Rome, Cardinal Ugo Poletti, "in the face of such a conspicuous sum, gave his blessing" to the controversial interment of Enrico De Pedis, the former boss of Rome's notorious Magliana gang. The money was reportedly used on missions and to restore the Basilica of St Apollinare, where the mobster was laid to rest next to popes and cardinals after his death in 1990.

The claims, which the Vatican has not commented on, may explain how such a reviled criminal was buried in such a hallowed site. Last week, to deflect growing criticism and to help resolve a 30-year-old murder mystery, it emerged that Vatican officials had decided to move the remains of De Pedis from his special crypt.

Pressure mounted earlier this month when a prosecuting magistrate, Giancarlo Capaldo, claimed senior officials at the Vatican knew much more than they were letting on about the Magliana gang's links to the Holy See, and the gang's suspected kidnap and murder of Emanuela Orlandi, the 15-year-old daughter of a Vatican official, in 1983. "There are people still alive, and still inside the Vatican, who know the truth," he said. Some believe Emanuela's father had evidence linking the Vatican Bank, Istituto per le Opere di Religione, to organised crime, and that she was snatched to keep him silent. The theory is that De Pedis, who was shot dead in 1990, organised the kidnapping.

For the past two decades, there has been speculation that Emanuela's remains were put in the tomb alongside De Pedis. The girl's brother, Pietro Orlandi, has joined those calling for the tomb to be opened.

The Vatican – under heavy scrutiny after a set of scandals – denies the claims and has hinted that investigators will be able to witness the re-opening of the crypt, in a bid to quash the rumours. "It seems that nothing has been concealed and there are no Vatican secrets to reveal," said a spokesman for Vatican, Father Federico Lombardin.

It is likely that the body of De Pedis will be moved to a less high-profile place of rest. The location may be decided at an upcoming meeting. Even if the girl's remains are not found in the crypt, the mystery surrounding her disappearance will remain.

Other theories surrounding her fate are not in short supply. One, more palatable for the Vatican, suggests that Magliana gang members snatched her at the behest of Turkish extremists, who wanted to use her as a bargaining tool to win the release of Mehmet Ali Agca, the Turkish gunman who tried to kill Pope John Paul II in 1981.

But others have implicated Paul Marcinkus, the disgraced and deceased former head of the Vatican bank, which was involved in the bankruptcy of Italy's largest private bank, the Banco Ambrosiano, in 1982.

Soon after the news of the scandal became public, the president of Banco Ambrosiano, Roberto Calvi, was found hanging beneath Blackfriars Bridge in London.